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I am using RStudio 0.98.501 and MacTex 2013 to run an analysis and compile a manuscript. In my setup, I use a master.rnw file that defines the LaTeX template. This file inputs a few manuscript .tex files that collaborators contribute to (they actually work in Word and I convert to .tex, but that is not important here).

To keep things clean in the master.rnw, I code the analysis in a child .rnw file and write my analysis manuscript text in the same child file. It's easy to define an object in an R code chunk in this child .rnw file, e.g., result <- 1+2 and reference this object in the child .rnw text, e.g., \Sexpr{result}.

I encountered a situation where I wanted to reference an analysis object before running the analysis child .rnw file—reporting a basic N=100 in the separate methods section .tex–so I tried two ways of running my basic analysis from the master.rnw file before inputting the methods.tex file that references the objects: (a) running a child file that sources a .R file and (b) sourcing the .R file from a code chunk in the master.rnw file. I don't think there should be a difference in outcomes. In my case there is not: they both fail.

LaTeX does not recognize the R objects when referenced in a .tex file I include. Of course it does fine when I reference an R object from within the master.rnw file. Is there a way to use \Sexpr in a .tex file and have LaTeX grab the R object?

I created a minimal example and uploaded the files to GitHub if anyone wants to take a crack at it.

% Knitr child example

<<knitr, include=FALSE>>=
  library(knitr)
  opts_knit$set(self.contained=FALSE)
@

\documentclass{article}
\begin{document}

% run analysis and reference objects, codeA and codeB, via \Sexpr{} in methods.tex that is included later

% attempt 1: run source file defining codeA object via a child rnw file
<<pre-results1, child='child1.rnw', include=FALSE>>=
# child1.rnw runs source("codeA.R")
@

% attempt 2: run source file defining codeB object directly
<<pre-results2>>=
  source("codeB.R")
@

% Methods section from tex file
\input{methods}
% in this file we try to grab the two objects codeA and codeB
% Referencing codeA: \Sexpr{codeA}
% Referencing codeB: \Sexpr{codeB}

\section*{Results}
% we know this works: define codeC and reference in the master file
<<results>>=
  codeC <- 5
  print(codeC)
@

Referencing codeC: \Sexpr{codeC}

\end{document}
Eric Green
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  • I haven't tested but doesn't it work to rename `methods.tex` to `methods.rnw` and include it by `child`? – kohske Apr 10 '14 at 00:43

1 Answers1

2

knit doesn't parse tex commands, so methods.tex will not be read out at knitting-time.

For workaround, try this:

<<knitr, include=FALSE>>=
  library(knitr)
  opts_knit$set(self.contained=FALSE)
  file.copy("methods.tex", "methods.rnw")
@

\documentclass{article}
\begin{document}

<<pre-results1, child='child.rnw', include=FALSE>>=
@
<<pre-results2>>=
  source("codeB.R")
@

% Methods section from rnw file
<<child="methods.rnw">>=
@ 

\end{document}
kohske
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